Retinal development, normal function, and disease are controlled, to a large extent, by the pattern of genes expressed by the cells of the retina. Gene expression can be modified by the local chromatin configuration of a gene. DNA methylation and histone modification, known as epigenetic modifications, can effect gene expression, and although they can be persistent and heritable, they do not directly change the primary DNA sequence. Despite the significant advances being made in understanding the role of epigenetics in gene regulation in other fields, little is known about the relationship between DNA methylation and tissue-specific gene expression in the developing and adult retina. Our preliminary studies show that, in the adult mouse, the region around the transcription start site of murine genes Rbp3 (PR-specific) and Rho (rod-specific) is hypomethylated in expressing photoreceptor cells and methylated in non-expressing cells from the inner nuclear layer. Presumably, these different patterns are established at some point between when the retinal cells are dividing neuroblasts and when they have undergone terminal division and begin to express cell-specific markers. The timing of the onset of this differential methylation found in two cell types originating from a common precursor is unknown. The research outlined in this exploratory proposal will provide a detailed molecular description of the high resolution the DNA methylation pattern around the transcription start site of two model PR-specific genes, Rbp3 and Rho, and how that methylation status changes during development. Genome-wide array experiments will examine tissue-specific DNA methylation patterns in the adult and developing retina, and will explore the hypothesis that retinal degeneration may be associated with changing patterns of retinal DNA methylation. Together, these studies will provide the necessary fundamental knowledge and set the stage for future mechanistic studies exploring the role of epigenetic mechanisms in retinal development and disease. PUBLIC HEALTH RELEVANCE: The ability of epigenetic mechanisms, such as DNA methylation, to initiate and maintain control of gene expression in the retina offers an entirely new frontier for exploration. Understanding the relationship between DNA methylation and tissue-specific gene expression in the developing and adult retina and exploring the role of DNA methylation in the molecular pathogenesis of retinal disease could someday have a significant impact on how we treat blinding diseases.